N - mixture models by species

modelling N by site to get relative abundance

abundance by site will be used as a cov on predator occupancy

7 models evaluated, dot, jdt + jdtSQ, lure + jdt + jdtSQ


Species:      AmericanPika



Metadata Summary:

N_sites N_counts N_detections rep_period iterations burnin thin
127 137 59 7 days 120000 20000 10



Detections by Year:

Yr 2016 2017 2018 2019 2020
sites 19 31 19 32 26
detections 5 10 0 24 20
N.dot.model 2 5 0 11 6



WAIC

Models by WAIC:
model description WAIC N.total.est
fm7 counts 3.889332 108
fm4 lure + jdt 358.924599 24
fm2 jdt 359.814351 25
fm6 lure + jdt + jdtSq 360.277323 24
fm5 jdt + jdtSq 360.763399 25
fm3 lure 368.539468 25
fm1 dot 370.195910 24



Model summaries:



model: fm1
dot



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
p[1] NA 8453 0.131 0.116 0.04 0.21 0 1.0009
p[2] NA 6013 0.074 0.062 0.03 0.12 0 1.0009
p[3] NA 10000 0.488 0.272 0.00 0.88 0 0.9843
p[4] NA 6132 0.060 0.055 0.03 0.09 0 1.001
p[5] NA 7934 0.127 0.124 0.08 0.17 0 1.001
lambda[1] NA 8919 0.123 0.066 0.01 0.24 0 0.9932
lambda[2] NA 4129 0.243 0.169 0.05 0.41 0 1.001
lambda[3] NA 10000 0.000 err 0.00 0.00 err err
lambda[4] NA 5803 0.503 0.423 0.22 0.76 0 1.001
lambda[5] NA 10000 0.273 0.226 0.09 0.44 0 1.001
N[121] NA 10092 0.033 err 0.00 0.00 err err
N[63] NA 0 0.000 err 0.00 0.00 err err
N[107] NA 9373 0.004 err 0.00 0.00 err err
N[39] NA 8014 0.073 err 0.00 0.00 err err
N[88] NA 9187 0.085 err 0.00 0.00 err err

p[1]

p[2]

p[3]

p[4]

p[5]

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[121]

N[63]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[107]

N[39]

N[88]







model: fm2
jdt



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha jdt 8406 0.448 0.439 0.22 0.67 0.00618 1.0004
alpha0 NA 6449 -2.611 -2.607 -2.93 -2.29 0 1.001
lambda[1] NA 10000 0.127 0.07 0.01 0.24 0 0.9939
lambda[2] NA 10000 0.222 0.17 0.06 0.37 0 1.0008
lambda[3] NA 10000 0.000 err 0.00 0.00 err err
lambda[4] NA 10648 0.417 0.391 0.20 0.62 0 1.001
lambda[5] NA 9240 0.359 0.294 0.13 0.57 0 1.001
N[105] NA 9473 0.029 err 0.00 0.00 err err
N[83] NA 10107 0.079 err 0.00 0.00 err err
N[107] NA 9739 0.028 err 0.00 0.00 err err
N[101] NA 8248 0.012 err 0.00 0.00 err err
N[119] NA 10000 0.108 err 0.00 0.00 err err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[105]

N[83]

N[107]

N[101]

N[119]

alpha relationship







model: fm3
lure



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha lure 10175 -0.113 -0.095 -0.36 0.11 0.76814 0.7752
alpha0 NA 7183 -2.463 -2.45 -2.75 -2.17 0 1.001
lambda[1] NA 10000 0.131 0.073 0.01 0.25 0 0.9939
lambda[2] NA 10000 0.206 0.151 0.05 0.34 0 1.0009
lambda[3] NA 10000 0.000 err 0.00 0.00 err err
lambda[4] NA 9188 0.413 0.373 0.19 0.61 0 1.001
lambda[5] NA 9146 0.330 0.266 0.12 0.53 0 1.001
N[76] NA 9698 0.078 err 0.00 0.00 err err
N[55] NA 0 0.000 err 0.00 0.00 err err
N[58] NA 0 0.000 err 0.00 0.00 err err
N[2] NA 10000 0.021 err 0.00 0.00 err err
N[100] NA 9782 0.015 err 0.00 0.00 err err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[76]

N[55]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[58]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[2]

N[100]

alpha relationship







model: fm4
lure + jdt



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha[1] lureDays 6528 -0.409 -0.421 -0.68 -0.13 0.0605 0.9947
alpha[2] julianDt 5904 0.615 0.608 0.35 0.86 0 1.001
alpha0 NA 4550 -2.709 -2.705 -3.07 -2.35 0 1.001
lambda[1] NA 9103 0.117 0.061 0.01 0.23 0 0.9943
lambda[2] NA 9644 0.204 0.159 0.05 0.34 0 1.0008
lambda[3] NA 9247 0.000 err 0.00 0.00 err err
lambda[4] NA 8955 0.428 0.402 0.21 0.64 0 1.001
lambda[5] NA 5738 0.473 0.366 0.16 0.77 0 1.001
N[34] NA 10000 0.019 err 0.00 0.00 err err
N[125] NA 10000 0.452 0 0.00 1.00 1 err
N[36] NA 9284 0.021 err 0.00 0.00 err err
N[105] NA 8658 0.105 err 0.00 0.00 err err
N[14] NA 8077 0.009 err 0.00 0.00 err err

alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[34]

N[125]

N[36]

N[105]

N[14]







model: fm5
jdt + jdtSq



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha[1] julianDt 2240 0.212 0.193 -0.21 0.64 0.78346 0.7802
alpha[2] julianDtSq 2197 0.238 0.253 -0.14 0.60 0.61391 0.8431
alpha0 NA 7177 -2.659 -2.633 -2.97 -2.32 0 1.001
lambda[1] NA 9696 0.136 0.072 0.01 0.26 0 0.9934
lambda[2] NA 10650 0.218 0.169 0.06 0.37 0 1.0008
lambda[3] NA 10000 0.000 err 0.00 0.00 err err
lambda[4] NA 10175 0.413 0.376 0.20 0.61 0 1.001
lambda[5] NA 8986 0.370 0.302 0.14 0.59 0 1.001
N[51] NA 0 0.000 err 0.00 0.00 err err
N[18] NA 10022 0.020 err 0.00 0.00 err err
N[108] NA 10000 0.021 err 0.00 0.00 err err
N[31] NA 10000 0.014 err 0.00 0.00 err err
N[59] NA 0 0.000 err 0.00 0.00 err err

alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[51]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[18]

N[108]

N[31]

N[59]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

julian date relationship







model: fm6
lure + jdt + jdtSq



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha[1] lureDays 6082 -0.402 -0.384 -0.68 -0.11 0.06838 0.9913
alpha[2] julianDt 2289 0.434 0.349 -0.04 0.87 0.31698 0.9382
alpha[3] julianDtSq 2288 0.186 0.216 -0.20 0.55 0.71535 0.7844
alpha0 NA 4530 -2.749 -2.738 -3.11 -2.37 0 1.001
lambda[1] NA 10000 0.123 0.075 0.00 0.23 0 0.994
lambda[2] NA 9588 0.203 0.149 0.05 0.34 0 1.0008
lambda[3] NA 10000 0.000 err 0.00 0.00 err err
lambda[4] NA 8890 0.422 0.368 0.20 0.62 0 1.001
lambda[5] NA 5724 0.484 0.355 0.16 0.78 0 1.001
N[97] NA 10000 0.015 err 0.00 0.00 err err
N[12] NA 9555 0.009 err 0.00 0.00 err err
N[70] NA 10000 0.234 err 0.00 1.00 err err
N[49] NA 10000 0.007 err 0.00 0.00 err err
N[43] NA 10000 0.004 err 0.00 0.00 err err

alpha[1]

alpha[2]

alpha[3]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[97]

N[12]

N[70]

N[49]

N[43]







model: fm7
counts



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha counts 8863 6.601 5.766 4.57 8.64 0 1.001
alpha0 NA 9717 -7.644 -7.406 -9.21 -5.96 0 1.001
lambda[1] NA 4197 0.915 0.518 0.04 1.75 0 0.9931
lambda[2] NA 4909 0.921 0.647 0.22 1.59 0 1.0007
lambda[3] NA 1580 0.006 err 0.00 0.00 err err
lambda[4] NA 8177 0.974 0.91 0.46 1.46 0 1.001
lambda[5] NA 6460 0.940 0.757 0.30 1.56 0 1.0009
N[56] NA 1703 0.005 err 0.00 0.00 err err
N[15] NA 7057 0.905 0 0.00 2.00 1 err
N[27] NA 0 1.000 err 1.00 1.00 err err
N[35] NA 7512 0.884 0 0.00 2.00 1 err
N[117] NA 9099 0.914 0 0.00 2.00 1 err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[56]

N[15]

N[27]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[35]

N[117]

alpha relationship